3-149601710-A-AT

Variant names:

• chr3-149601710-A-AT
• rs3976504
• NM_015472.6:c.432-28711dupA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015472.6(WWTR1):​c.432-28711dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.063 (673 hom., cov: 0)
• Consequence: WWTR1 NM_015472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 0 publications found

Genes affected

WWTR1 (HGNC:24042): (WW domain containing transcription regulator 1) Enables transcription coactivator activity. Involved in several processes, including hippo signaling; positive regulation of cell differentiation; and regulation of signal transduction. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015472.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWTR1	NM_015472.6	MANE Select	c.432-28711dupA		intron	N/A	NP_056287.1	Q9GZV5
	WWTR1	NM_001168278.3		c.432-28711dupA		intron	N/A	NP_001161750.1	Q9GZV5
	WWTR1	NM_001168280.3		c.432-28711dupA		intron	N/A	NP_001161752.1	Q9GZV5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WWTR1	ENST00000360632.8	TSL:1 MANE Select	c.432-28711_432-28710insA		intron	N/A	ENSP00000353847.3	Q9GZV5
	WWTR1	ENST00000465804.5	TSL:2	c.432-28711_432-28710insA		intron	N/A	ENSP00000419465.1	Q9GZV5
	WWTR1	ENST00000467467.5	TSL:5	c.432-28711_432-28710insA		intron	N/A	ENSP00000419234.1	Q9GZV5

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9515 AN: 150594 Hom.: 671 Cov.: 0

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00617

Gnomad OTH AF: 0.0558

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0633 AC: 9533 AN: 150708 Hom.: 673 Cov.: 0 AF XY: 0.0652 AC XY: 4804 AN XY: 73640

African (AFR) AF: 0.149 AC: 6145 AN: 41146

American (AMR) AF: 0.0858 AC: 1302 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3460

East Asian (EAS) AF: 0.220 AC: 1133 AN: 5156

South Asian (SAS) AF: 0.0212 AC: 101 AN: 4760

European-Finnish (FIN) AF: 0.0249 AC: 252 AN: 10116

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.00617 AC: 417 AN: 67596

Other (OTH) AF: 0.0557 AC: 117 AN: 2102

Alfa AF: 0.00734 Hom.: 1335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3976504; hg19: chr3-149319497;